title: Brownian dynamics study of the association between the 70S ribosome and elongation factor G.
abstract: Protein synthesis on the ribosome involves a number of external protein factors that bind at its functional sites. One key factor is the elongation factor G (EF-G) that facilitates the translocation of transfer RNAs between their binding sites, as well as advancement of the messenger RNA by one codon. The details of the EF-G/ribosome diffusional encounter and EF-G association pathway still remain unanswered. Here, we applied Brownian dynamics methodology to study bimolecular association in the bacterial EF-G/70S ribosome system. We estimated the EF-G association rate constants at 150 and 300 mM monovalent ionic strengths and obtained reasonable agreement with kinetic experiments. We have also elucidated the details of EF-G/ribosome association paths and found that positioning of the L11 protein of the large ribosomal subunit is likely crucial for EF-G entry to its binding site.
authors.affiliation: Interdisciplinary Centre for Mathematical and Computational Modeling, University of Warsaw, Warsaw, Poland. M.Dlugosz@icm.edu.pl
authors.forename: Maciej
authors.initials: M
authors.lastname: Długosz
authors.forename: Gary A
authors.initials: GA
authors.lastname: Huber
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
authors.forename: Joanna
authors.initials: J
authors.lastname: Trylska
mesh_terms: D001665:Binding Sites; D003062:Codon; D003198:Computer Simulation; D004926:Escherichia coli / Q000378:metabolism*; D007477:Ions; D007700:Kinetics; D015233:Models, Statistical; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D020653:Peptide Elongation Factor G / Q000737:chemistry*; D012333:RNA, Messenger / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry; D012270:Ribosomes / Q000737:chemistry; D055672:Static Electricity; D016963:Thermus thermophilus / Q000378:metabolism
chemical_list: D003062:Codon; D007477:Ions; D020653:Peptide Elongation Factor G; D012333:RNA, Messenger; D012343:RNA, Transfer